[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Peter Cock]

On Fri, Feb 1, 2013 at 10:29 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Michiel, Peter, everyone,
>
>>> > I'm OK with using the setUp and tearDown arguments to
>>> > doctest.DocTestSuite to do the directory magic, but
>>> > keeping the test files
>>> > under Tests/.
>>>
>>> As a more elegant version of the Bio._utils.run_doctest()
>>> function?
>>
>> Exactly. Bow, do you want to give this approach a try?
>> (Assuming that there are no further objections from the other developers).
>
> Just to be clear, we are:
>
> * changing all module's doctest file path to use relative paths (with
> respect to the module's location),
> * replacing the run_doctest() import with a simpler doctest import and
> `doctest.testmod()` in each module having this doctest
> * resorting to setUp and tearDown in the DocTestSuite in
> `run_tests.py` so that each module / submodule can find their test
> files

That wasn't my understanding - I thought we we just talking about
making the Bio._utils.run_doctest() use setUp and tearDown to
take care of the path changes (although I'm not sure if that will
actually be any shorter - we'd find out).

> * and refactoring all string functions in Bio._utils to Bio.Phylo and
> Bio.SearchIO, so that we can remove Bio._utils,

I'm not particularly bothered either way on this. Having misc utilities
like this under Bio.Phylo or Bio.SearchIO makes is clear where they
are used, and makes it easier to compartmentalise functionality.

Regards,

Peter